mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
38 lines
1.3 KiB
Text
38 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process GATK_CREATESEQUENCEDICTIONARY {
|
|
tag "$fasta"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.1.9.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0"
|
|
} else {
|
|
container "quay.io/biocontainers/gatk4:4.1.9.0--py39_0"
|
|
}
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "*.dict" , emit: dict
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
gatk --java-options "-Xmx${task.memory.toGiga()}g" \\
|
|
CreateSequenceDictionary \\
|
|
--REFERENCE $fasta \\
|
|
$options.args
|
|
|
|
echo \$(gatk CreateSequenceDictionary --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|